Solar salterns are extreme environments of high scientific interest, hosting specialized microbial communities shaped by steep physicochemical gradients. Here we present the first comparative metagenomic analysis of two solar salterns in southern Sardinia: Conti Vecchi (active saltern, AS) and Molentargius (inactive saltern, IS), located ~20 km apart and exposed to similar climatic conditions. This setting provides a unique opportunity to assess the impact of saltwork management on microbial diversity along a salinity gradient.

Water and sediment samples were collected from ponds with varying salinities in winter and summer, yielding 2786 metagenome-assembled genomes (MAGs; 1537 from AS and 1249 from IS; 1131 from sediments and 1655 from water). Seasonal variation was the primary driver of environmental differences (61% of variance, p-value < 0.001), although site-specific differences in thermal range and pond structure were also observed.

Benthic trophic conditions were instead driven mainly by pond identity within each saltern (31% of variance, p-value < 0.001), with no significant effect of saltern or season. In the AS, the medium-low salinity pond was eutrophic, with organic carbon exceeding microbial processing capacity, while the high-salinity pond showed near-complete depletion of biopolymeric carbon, displaying oligotrophic features. Metagenomic results supported these patterns, with Pseudomonadota and Bacteroidota dominating at low salinities, and Halobacteriota prevailing in high-salinity ponds. In the IS, the high salinity pond exhibited a different pattern: despite comparable salinity to the AS hypersaline pond, it had markedly higher carbon degradation rates and faster turnover time in winter, with the opposite trend in summer.

This points to a distinct microbial community, confirmed taxonomically by an unexpected dominance of Bacteria - including Cyanobacteria - despite the high salinity. This contrast may reflect differences in saltwork management: the controlled water level in AS produced a solid crust of salt, whereas the less controlled level in the IS produced a gypsum crust with a visible green layer.

A large fraction of MAGs could not be assigned to known taxa, pointing to unexpected novelty from species to higher taxonomic levels and positioning southern Sardinia salterns as promising reservoirs of prokaryotic diversity for future investigation of under-characterized Mediterranean extreme environments.